Systems Metabolic Engineering

Methods and Protocols

Editors:

ISBN: 978-1-62703-298-8 (Print) 978-1-62703-299-5 (Online)

Table of contents (23 protocols)

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  1. Front Matter

    Pages i-xii

  2. Modeling and Simulation Tools

    1. Front Matter

      Pages 1-1

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      Book Protocol

      Pages 3-16

      Genome-Scale Model Management and Comparison

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      Pages 17-45

      Automated Genome Annotation and Metabolic Model Reconstruction in the SEED and Model SEED

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      Pages 47-59

      Metabolic Model Refinement Using Phenotypic Microarray Data

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      Pages 61-83

      Linking Genome-Scale Metabolic Modeling and Genome Annotation

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      Pages 85-101

      Resolving Cell Composition Through Simple Measurements, Genome-Scale Modeling, and a Genetic Algorithm

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      Pages 103-112

      A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism)

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      Pages 113-121

      Kinetic Modeling of Metabolic Pathways: Application to Serine Biosynthesis

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      Pages 123-147

      Computational Tools for Guided Discovery and Engineering of Metabolic Pathways

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      Pages 149-173

      Retrosynthetic Design of Heterologous Pathways

  3. Genome Engineering Tools

    1. Front Matter

      Pages 175-175

    2. No Access

      Book Protocol

      Pages 177-209

      Customized Optimization of Metabolic Pathways by Combinatorial Transcriptional Engineering

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      Pages 211-222

      Adaptive Laboratory Evolution for Strain Engineering

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      Pages 223-246

      Trackable Multiplex Recombineering for Gene-Trait Mapping in E. coli

  4. Systems-Level ‘Omics Tools

    1. Front Matter

      Pages 247-247

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      Pages 249-267

      Identification of Mutations in Evolved Bacterial Genomes

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      Pages 269-295

      Discovery of Posttranscriptional Regulatory RNAs Using Next Generation Sequencing Technologies

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      Pages 297-334

      13C-Based Metabolic Flux Analysis: Fundamentals and Practice

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      Pages 335-351

      Nuclear Magnetic Resonance Methods for Metabolic Fluxomics

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      Pages 353-365

      Using Multiple Tracers for 13C Metabolic Flux Analysis

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      Pages 367-390

      Isotopically Nonstationary 13C Metabolic Flux Analysis

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      Pages 391-406

      Sample Preparation and Biostatistics for Integrated Genomics Approaches

  5. Integrating Large Datasets for Modeling and Engineering Applications

    1. Front Matter

      Pages 407-407

    2. No Access

      Book Protocol

      Pages 409-428

      Targeted Metabolic Engineering Guided by Computational Analysis of Single-Nucleotide Polymorphisms (SNPs)

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